Exploring Cranberry Microbiome: Fungal and Bacterial Communities in Fruit and Soil from Wild and Managed Systems

Abstract Text: Cranberry fruit rot (CFR) has been a significant constraint in cranberry cultivation since the late 1800s. A century of research across growing regions has linked 10–15 fungi to CFR, but the role of bacteria remains unclear. Also, no prior studies have compared the microbiomes of visibly healthy versus rotten fruit or differences between soil and fruit microbiomes. We investigated bacterial and fungal microbiomes in healthy and rotten fruit, as well as in soils from wild, organic, and conventional systems, using high-throughput sequencing. Results indicate that healthy berries hosted diverse microbial communities dominated by Proteobacteria and various yeasts, with similar diversity across ecosystems. In rotten berries, microbial profiles shifted dramatically: acetic acid bacteria proliferated, with Gluconobacter increasing from 5.8% in healthy fruit to 26.2% in rot, while beneficial bacteria declined, exemplified by Rhodococcus dropping from 0.8% to 0.16%. Fungal abundance spiked as fruit decayed; Phomopsis rose from 0.5% to 4.0%, becoming dominant, while Colletotrichum similarly proliferated, and generalist fungi like Alternaria declined from 1.8% to 0.5%. Rotten fruit from organic bogs harbored the highest bacterial richness, while conventional bogs showed intermediate levels. In contrast, wild rotten fruit exhibited the greatest fungal richness, significantly higher than organic or conventional systems, and contained a distinct fungal community. These ecosystem differences highlight the need to leverage microbiome diversity for improved cranberry disease management.